X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FAWSThread.java;h=2e3ddddbfcd3a17ee33206b051bc7d57bf1e6bdd;hb=1ef93cb2817f75699773f049b8d25e5b509c2830;hp=0167690aa3db669b5dc359e14792c4eed3f691f7;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index 0167690..2e3dddd 100644
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.java
@@ -1,24 +1,26 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
@@ -26,7 +28,11 @@ import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.WebserviceInfo;
-import jalview.gui.FeatureRenderer.FeatureRendererSettings;
+import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
+
+import java.util.ArrayList;
+import java.util.List;
public abstract class AWSThread extends Thread
{
@@ -54,7 +60,7 @@ public abstract class AWSThread extends Thread
/**
* dataset sequence relationships to be propagated onto new results
*/
- protected AlignedCodonFrame[] codonframe = null;
+ protected List codonframe = null;
/**
* are there jobs still running in this thread.
@@ -84,9 +90,15 @@ public abstract class AWSThread extends Thread
*/
protected String WsUrl = null;
+ /*
+ * The AlignFrame from which the service was requested.
+ */
+ private AlignFrame alignFrame;
+
/**
* generic web service job/subjob poll loop
*/
+ @Override
public void run()
{
JobStateSummary jstate = null;
@@ -115,16 +127,16 @@ public abstract class AWSThread extends Thread
throw (new Exception(
"Timed out when communicating with server\nTry again later.\n"));
}
- jalview.bin.Cache.log.debug("Job " + j + " Result state "
- + jobs[j].getState() + "(ServerError="
- + jobs[j].isServerError() + ")");
+ Console.debug("Job " + j + " Result state " + jobs[j].getState()
+ + "(ServerError=" + jobs[j].isServerError() + ")");
} catch (Exception ex)
{
// Deal with Transaction exceptions
- wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName
- + " Server exception!\n" + ex.getMessage());
+ wsInfo.appendProgressText(jobs[j].jobnum, MessageManager
+ .formatMessage("info.server_exception", new Object[]
+ { WebServiceName, ex.getMessage() }));
// always output the exception's stack trace to the log
- Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
+ Console.warn(WebServiceName + " job(" + jobs[j].jobnum
+ ") Server exception.");
// todo: could limit trace to cause if this is a SOAPFaultException.
ex.printStackTrace();
@@ -132,7 +144,7 @@ public abstract class AWSThread extends Thread
if (jobs[j].allowedServerExceptions > 0)
{
jobs[j].allowedServerExceptions--;
- Cache.log.debug("Sleeping after a server exception.");
+ Console.debug("Sleeping after a server exception.");
try
{
Thread.sleep(5000);
@@ -142,7 +154,7 @@ public abstract class AWSThread extends Thread
}
else
{
- Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
+ Console.warn("Dropping job " + j + " " + jobs[j].jobId);
jobs[j].subjobComplete = true;
wsInfo.setStatus(jobs[j].jobnum,
WebserviceInfo.STATE_STOPPED_SERVERERROR);
@@ -154,10 +166,10 @@ public abstract class AWSThread extends Thread
jobs[j].clearResponse(); // may contain out of date result data
wsInfo.setStatus(jobs[j].jobnum,
WebserviceInfo.STATE_STOPPED_ERROR);
- Cache.log.error("Out of memory when retrieving Job " + j
- + " id:" + WsUrl + "/" + jobs[j].jobId, er);
- new jalview.gui.OOMWarning("retrieving result for "
- + WebServiceName, er);
+ Console.error("Out of memory when retrieving Job " + j + " id:"
+ + WsUrl + "/" + jobs[j].jobId, er);
+ new jalview.gui.OOMWarning(
+ "retrieving result for " + WebServiceName, er);
System.gc();
}
}
@@ -172,10 +184,9 @@ public abstract class AWSThread extends Thread
Thread.sleep(5000);
} catch (InterruptedException e)
{
- Cache.log
- .debug("Interrupted sleep waiting for next job poll.", e);
+ Console.debug("Interrupted sleep waiting for next job poll.", e);
}
- // System.out.println("I'm alive "+alTitle);
+ // jalview.bin.Console.outPrintln("I'm alive "+alTitle);
}
}
if (jobComplete && jobs != null)
@@ -184,10 +195,11 @@ public abstract class AWSThread extends Thread
}
else
{
- Cache.log
- .debug("WebServiceJob poll loop finished with no jobs created.");
- wsInfo.setStatus(wsInfo.STATE_STOPPED_ERROR);
- wsInfo.appendProgressText("No jobs ran.");
+ Console.debug(
+ "WebServiceJob poll loop finished with no jobs created.");
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ wsInfo.appendProgressText(
+ MessageManager.getString("info.no_jobs_ran"));
wsInfo.setFinishedNoResults();
}
}
@@ -292,13 +304,12 @@ public abstract class AWSThread extends Thread
SequenceI[] alignment = al.getSequencesArray();
for (int sq = 0; sq < alignment.length; sq++)
{
- for (int i = 0; i < codonframe.length; i++)
+ for (AlignedCodonFrame acf : codonframe)
{
- if (codonframe[i] != null
- && codonframe[i].involvesSequence(alignment[sq]))
+ final SequenceI seq = alignment[sq];
+ if (acf != null && acf.involvesSequence(seq))
{
- al.addCodonFrame(codonframe[i]);
- codonframe[i] = null;
+ al.addCodonFrame(acf);
break;
}
}
@@ -357,7 +368,7 @@ public abstract class AWSThread extends Thread
AlignmentView alview, String wsurl2)
{
super();
- // this.alignFrame = alframe;
+ this.alignFrame = alframe;
currentView = alframe.getCurrentView().getAlignment();
featureSettings = alframe.getFeatureRenderer().getSettings();
defGapChar = alframe.getViewport().getGapCharacter();
@@ -366,13 +377,18 @@ public abstract class AWSThread extends Thread
WsUrl = wsurl2;
if (alframe != null)
{
- AlignedCodonFrame[] cf = alframe.getViewport().getAlignment()
+ List cf = alframe.getViewport().getAlignment()
.getCodonFrames();
if (cf != null)
{
- codonframe = new AlignedCodonFrame[cf.length];
- System.arraycopy(cf, 0, codonframe, 0, cf.length);
+ codonframe = new ArrayList();
+ codonframe.addAll(cf);
}
}
}
+
+ protected AlignFrame getRequestingAlignFrame()
+ {
+ return this.alignFrame;
+ }
}